CONNparticipantIDs

% This will extract BIDS format participant IDs (e.g., sub-001) and save it as a covariate in CONN. This helps with data organization because CONN just lists subjects numerically but does not list the participant IDs.

% Load functional MRI data into CONN
functional_files = conn_module('get', 'functionals');

% Initialize a cell array to store IDs
IDs = cell(length(functional_files), 1);

% Loop through each functional file to extract subject ID
for i = 1:length(functional_files)
    % If the cell is 1x2, pick the first content
    if iscell(functional_files{i}) && length(functional_files{i}) == 2
        file = functional_files{i}{1};
    else
        file = functional_files{i};
    end
    
    % Display the current file to debug
    disp(['Processing file: ', file]);
    
    % Extract the subject ID using regular expression
    ID = regexp(file, '(?<=sub-)\d+', 'match', 'once');
    if ~isempty(ID)
        IDs{i} = str2double(ID);
    else
        IDs{i} = NaN; % Assign NaN if ID extraction fails
    end
end

% Convert the cell array to a numeric array, handling NaNs if necessary
IDs = cell2mat(IDs);

% Display the extracted subject IDs
disp('Subject IDs:');
disp(IDs);

% Save the subject IDs into CONN for safekeeping
conn_module('set', 'l2covariates', IDs(:), {'ID'}, {'IDs read from filenames'}, true);